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Background and AimsThe Lythraceae are a mainly subtropical to tropical family of the order Myrtales with 28 currently accepted genera and approximately 600 species. There is currently no well-supported phylogenetic and biogeographical hypothesis of the Lythraceae incorporating all currently accepted genera, which we sought to provide.MethodsPlastomes of representative species of 18 distinct Lythraceae genera were sequenced and annotated. Together with existing sequences, plastomes of all 28 currently accepted genera in the Lythraceae were brought together for the first time. The plastomes were aligned and a Bayesian phylogenetic hypothesis was produced. We then conducted a time-calibrated Bayesian analysis and a biogeographical analysis.Key ResultsPlastome-based Bayesian and maximum-likelihood phylogenetic trees are generally congruent with recent nuclear phylogenomic data and resolve two deeply branching major clades in the Lythraceae. One major clade concentrates shrubby and arboreal South American and African genera that inhabit seasonally dry environments, with larger, often winged seeds, adapted to dispersal by the wind. The second major clade concentrates North American, Asian, African and several near-cosmopolitan herbaceous, shrubby and arboreal genera, often inhabiting humid or aquatic environments, with smaller seeds possessing structures that facilitate dispersal by water.ConclusionsWe hypothesize that the Lythraceae dispersed early in the Late Cretaceous from South American to North American continents, with subsequent expansion in the Late Cretaceous of a North American lineage through Laurasia to Africa via a boreotropical route. Two later expansions of South American clades to Africa in the Palaeocene and Eocene, respectively, are also hypothesized. Transoceanic dispersal in the family is possibly facilitated by adaptations to aquatic environments that are common to many extant genera of the Lythraceae, where long-distance dispersal and vicariance may

Brassica oleracea displays enormous phenotypic variation, including vegetables like cabbage, broccoli, cauliflower, kohlrabi, kales etc. Its domestication has not been clarified, despite several genetic studies and investigations of ancient literature. We used 14 152 high-quality SNP markers for population genetic studies and species-tree estimation (treating morphotypes as “species”) using SVD-quartets coalescent-modelling of a collection of 912 globally distributed accessions representing ten morphotypes of B. oleracea, wild B. oleracea accessions and nine related C9 Brassica species. Our genealogical tree provided evidence for two domestication lineages, the “leafy head” lineage (LHL) and the “arrested inflorescence” lineage (AIL). It also showed that kales are polyphyletic with regards to B. oleracea morphotypes, which fits ancient literature describing highly diverse kale types at around 400 BC. The SVD-quartets species tree topology showed that different kale clades are sister to either the LHL or the AIL. Cabbages from the middle-east formed the first-branching cabbage-clade, supporting the hypothesis that cabbage domestication started in the middle-east, which is confirmed by archeological evidence and historic writings. We hypothesize that cabbages and cauliflowers stem from kales introduced from Western Europe to the middle-east, possibly transported with the tin-trade routes in the Bronze age, to be re-introduced later into Europe. Cauliflower is the least diverse morphotype showing strong genetic differentiation with other morphotypes except broccoli, suggesting a strong genetic bottleneck. Genetic diversity reduced from landraces to modern hybrids for almost all morphotypes. This comprehensive Brassica C-group germplasm collection provides valuable genetic resources and a sound basis for B. oleracea breeding.

The repetitive part of the genome (the repeatome) contains a wealth of often overlooked information that can be used to resolve phylogenetic relationships and test evolutionary hypotheses for clades of related plant species such as Pelargonium. We have generated genome skimming data for 18 accessions of Pelargonium section Ciconium and one outgroup. We analyzed repeat abundancy and repeat similarity in order to construct repeat profiles and then used these for phylogenetic analyses. We found that phylogenetic trees based on read similarity were largely congruent with previous work based on morphological and chloroplast sequence data. For example, results agreed in identifying a "Core Ciconium" group which evolved after the split with P. elongatum. We found that this group was characterized by a unique set of repeats, which confirmed currently accepted phylogenetic hypotheses. We also found four species groups within P. sect. Ciconium that reinforce previous plastome-based reconstructions. A second repeat expansion was identified in a subclade which contained species that are considered to have dispersed from Southern Africa into Eastern Africa and the Arabian Peninsula. We speculate that the Core Ciconium repeat set correlates with a possible WGD event leading to this branch.

The consequences of the Cretaceous–Paleogene (K–Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KPB may have played a role in survival and subsequent diversification of plant lineages. To gain new insights into the origins of Cenozoic biodiversity, we examine the origin and early evolution of the globally diverse legume family (Leguminosae or Fabaceae). Legumes are ecologically (co-)dominant across many vegetation types, and the fossil record suggests that they rose to such prominence after the KPB in parallel with several well-studied animal clades including Placentalia and Neoaves. Furthermore, multiple WGD events are hypothesized to have occurred early in legume evolution. Using a recently inferred phylogenomic framework, we investigate the placement of WGDs during early legume evolution using gene tree reconciliation methods, gene count data and phylogenetic supernetwork reconstruction. Using 20 fossil calibrations we estimate a revised timeline of legume evolution based on 36 nuclear genes selected as informative and evolving in an approximately clock-like fashion. To establish the timing of WGDs we also date duplication nodes in gene trees. Results suggest either a pan-legume WGD event on the stem lineage of the family, or an allopolyploid event involving (some of) the earliest lineages within the crown group, with additional nested WGDs subtending subfamilies Papilionoideae and Detarioideae. Gene tree reconciliation methods that do not account for allopolyploidy may be misleading in inferring an earlier WGD event at the time of divergence of the two parental lineages of the polyploid, suggesting that the allopolyploid scenario is more likely. We show that the crown age of the legumes dates to the Maastr, SCOPUS: ar.j, info:eu-repo/semantics/published

The consequences of the Cretaceous–Paleogene (K–Pg) boundary (KPB) mass extinction for the evolution of plant diversity remain poorly understood, even though evolutionary turnover of plant lineages at the KPB is central to understanding assembly of the Cenozoic biota. The apparent concentration of whole genome duplication (WGD) events around the KPB may have played a role in survival and subsequent diversification of plant lineages. To gain new insights into the origins of Cenozoic biodiversity, we examine the origin and early evolution of the globally diverse legume family (Leguminosae or Fabaceae). Legumes are ecologically (co-)dominant across many vegetation types, and the fossil record suggests that they rose to such prominence after the KPB in parallel with several well-studied animal clades including Placentalia and Neoaves. Furthermore, multiple WGD events are hypothesized to have occurred early in legume evolution. Using a recently inferred phylogenomic framework, we investigate the placement of WGDs during early legume evolution using gene tree reconciliation methods, gene count data and phylogenetic supernetwork reconstruction. Using 20 fossil calibrations we estimate a revised timeline of legume evolution based on 36 nuclear genes selected as informative and evolving in an approximately clock-like fashion. To establish the timing of WGDs we also date duplication nodes in gene trees. Results suggest either a pan-legume WGD event on the stem lineage of the family, or an allopolyploid event involving (some of) the earliest lineages within the crown group, with additional nested WGDs subtending subfamilies Papilionoideae and Detarioideae. Gene tree reconciliation methods that do not account for allopolyploidy may be misleading in inferring an earlier WGD event at the time of divergence of the two parental lineages of the polyploid, suggesting that the allopolyploid scenario is more likely. We show that the crown age of the legumes dates to the Maastrichtian o